# Analysis ID : Project XYZ Preliminary Population PK Analysis
# Purpose : Initial Target Attainment Assessment
# Other Info : Define your own!
library(flextable)
library(plotly)
library(DT)
The purpose of this data memo is to provide a summary of the base population pharmacokinetic model fit for study XYZ.
library(DT)
finaldat <- read.csv(file='./data/finaldat.csv')
DT::datatable(finaldat, rownames = FALSE, filter = "top",
options = list(pageLength = 5, scrollX = TRUE))
dm_table <- readRDS(file='./tables/dmtable.RDS')
dm_table
Characteristic | N | N = 1501 |
|---|---|---|
AGE | 150 | 50.5 (38.0 - 61.0) |
SEX | 150 | |
F | 45 (30%) | |
M | 105 (70%) | |
RACE | 150 | |
ASIAN | 21 (14%) | |
BLACK | 36 (24%) | |
OTHER | 33 (22%) | |
WHITE | 60 (40%) | |
WT | 150 | 71 (55 - 94) |
1Mean (Range); n (%) | ||
mean_conctable <- readRDS(file='./tables/mean_conctable.RDS')
mean_conctable
Dose Group | |||
|---|---|---|---|
Time (hr) | 5000 μg | 10000 μg | 20000 μg |
0.00 | 0 (0-0) | 0 (0-0) | 0 (0-0) |
0.25 | 19.5 (5.19-56.4) | 38.8 (4.77-111) | 58.3 (6.83-164) |
0.50 | 32.6 (9.88-84.3) | 64.9 (19-167) | 96.9 (27.9-247) |
1.00 | 48.1 (17.2-119) | 96.3 (30.6-235) | 144 (41.1-349) |
2.00 | 56.2 (17.7-116) | 112 (32.7-236) | 169 (51.7-352) |
3.00 | 55.8 (19.8-118) | 112 (37.7-235) | 167 (56-348) |
4.00 | 51.7 (15.4-131) | 103 (27.5-264) | 155 (37.8-400) |
6.00 | 41.2 (9.77-91.4) | 82.4 (14.3-182) | 124 (21.9-270) |
8.00 | 34.7 (9.36-67) | 69.9 (21.7-136) | 104 (29.8-199) |
12.00 | 25 (2.98-69.8) | 49.6 (5.06-140) | 75.8 (8.52-208) |
16.00 | 18.7 (1.08-57.5) | 37.5 (0-115) | 56.8 (0-169) |
24.00 | 9.52 (0.103-32.9) | 19.3 (0-67.3) | 28.1 (0-99.8) |
time_conc <- readRDS(file='./plots/time_concentration_by_subject.RDS')
time_conc
time_conc <- readRDS(file='./plots/time_concentration_by_subject.RDS')
time_conc |>
plotly::ggplotly()
time_conc_dose_grp <- readRDS(file='./plots/time_concentration_facet_dose_group.RDS')
time_conc_dose_grp
time_conc_dose_grp <- readRDS(file='./plots/time_concentration_facet_dose_group.RDS')
time_conc_dose_grp |>
plotly::ggplotly()
time_conc_wt <- readRDS(file='./plots/time_concentration_by_subject_by_wt_cut.RDS')
time_conc_wt
time_conc_wt <- readRDS(file='./plots/time_concentration_by_subject_by_wt_cut.RDS')
time_conc_wt |>
plotly::ggplotly()
## View the overall tables
overall_table_cmpt_scenarios <- readRDS("./tables/overall_table_cmpt_scenarios.RDS")
overall_table_cmpt_scenarios
Model | -2LL | AIC | BIC | nParm | nObs | nSub | EpsShrinkage |
|---|---|---|---|---|---|---|---|
OneCpt | 13,488.16 | 13,502.16 | 13,540.02 | 7 | 1,650 | 150 | 0.12219 |
TwoCpt | 13,489.52 | 13,511.52 | 13,571.01 | 11 | 1,650 | 150 | 0.12263 |
ThreeCpt | 13,487.59 | 13,517.59 | 13,598.72 | 15 | 1,650 | 150 | 0.12203 |
dvpred <- readRDS("./plots/one_cmpt_dv_preds_idv.RDS")
dvpred
dvpred <- readRDS("./plots/one_cmpt_dv_preds_idv.RDS")
dvpred |>
plotly::ggplotly()
cwrespred <- readRDS("./plots/one_cmpt_res_vs_pred.RDS")
cwrespred
cwrespred <- readRDS("./plots/one_cmpt_res_vs_pred.RDS")
cwrespred |>
plotly::ggplotly()
table_theta <- readRDS("./tables/one_cmpt_theta.RDS")
table_theta
Name | Label | Value | SE | RSE% | 2.5% CI | 97.5% CI |
|---|---|---|---|---|---|---|
THETA(1) | tvKa | 1.17 | 0.03 | 2.95 | 1.11 | 1.24 |
THETA(2) | tvV | 81.46 | 2.95 | 3.62 | 75.68 | 87.24 |
THETA(3) | tvCl | 7.95 | 0.41 | 5.16 | 7.15 | 8.76 |
table_omega <- readRDS("./tables/one_cmpt_omega.RDS")
table_omega
Name | Label | Value | SE | RSE% | Fixed | Diagonal | 2.5% CI | 97.5% CI | Shrinkage% |
|---|---|---|---|---|---|---|---|---|---|
OMEGA(1,1) | nKa | 0.081 | 0.014 | 17.625 | FALSE | TRUE | 0.053 | 0.109 | 21.728 |
OMEGA(2,2) | nV | 0.178 | 0.023 | 12.805 | FALSE | TRUE | 0.134 | 0.223 | 3.356 |
OMEGA(3,3) | nCl | 0.372 | 0.039 | 10.430 | FALSE | TRUE | 0.296 | 0.448 | 2.413 |
table_sigma <- readRDS("./tables/one_cmpt_sigma.RDS")
table_sigma
Name | Label | Value | SE | RSE% | Fixed | 2.5% CI | 97.5% CI | Shrinkage% |
|---|---|---|---|---|---|---|---|---|
SIGMA(1,1) | CEps | 0.207 | 0.010 | 4.783 | FALSE | 0.187 | 0.226 | 12.219 |
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.28 plotly_4.10.2 ggplot2_3.4.2 flextable_0.9.2
loaded via a namespace (and not attached):
[1] httr_1.4.6 sass_0.4.6 tidyr_1.3.0
[4] jsonlite_1.8.5 viridisLite_0.4.2 splines_4.2.1
[7] bslib_0.5.0 shiny_1.7.4 askpass_1.1
[10] fontLiberation_0.1.0 yaml_2.3.7 gdtools_0.3.3
[13] pillar_1.9.0 lattice_0.20-45 glue_1.6.2
[16] uuid_1.1-0 digest_0.6.31 promises_1.2.0.1
[19] polyclip_1.10-4 colorspace_2.1-0 Matrix_1.5-4.1
[22] htmltools_0.5.5 httpuv_1.6.11 gfonts_0.2.0
[25] fontBitstreamVera_0.1.1 pkgconfig_2.0.3 httpcode_0.3.0
[28] purrr_1.0.1 xtable_1.8-4 scales_1.2.1
[31] tweenr_2.0.2 later_1.3.1 officer_0.6.2
[34] fontquiver_0.2.1 ggforce_0.4.1 tibble_3.2.1
[37] openssl_2.0.6 mgcv_1.8-40 generics_0.1.3
[40] farver_2.1.1 ellipsis_0.3.2 cachem_1.0.8
[43] withr_2.5.0 lazyeval_0.2.2 cli_3.6.1
[46] magrittr_2.0.3 crayon_1.5.2 mime_0.12
[49] evaluate_0.21 fansi_1.0.4 nlme_3.1-157
[52] MASS_7.3-60 xml2_1.3.4 textshaping_0.3.6
[55] tools_4.2.1 data.table_1.14.8 lifecycle_1.0.3
[58] munsell_0.5.0 zip_2.3.0 compiler_4.2.1
[61] jquerylib_0.1.4 xpose_0.4.16 systemfonts_1.0.4
[64] rlang_1.1.1 grid_4.2.1 rstudioapi_0.14
[67] htmlwidgets_1.6.2 crosstalk_1.2.0 labeling_0.4.2
[70] rmarkdown_2.23 gtable_0.3.3 curl_5.0.1
[73] R6_2.5.1 knitr_1.43 dplyr_1.1.2
[76] fastmap_1.1.1 utf8_1.2.3 ragg_1.2.5
[79] crul_1.4.0 Rcpp_1.0.10 vctrs_0.6.3
[82] tidyselect_1.2.0 xfun_0.39